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de Freitas Magalhães B, Fan G, Sontag E, Josić K, Bennett MR. Pattern Formation and Bistability in a Synthetic Intercellular Genetic Toggle. ACS Synth Biol 2024; 13:2844-2860. [PMID: 39214591 DOI: 10.1021/acssynbio.4c00272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Differentiation within multicellular organisms is a complex process that helps to establish spatial patterning and tissue formation within the body. Often, the differentiation of cells is governed by morphogens and intercellular signaling molecules that guide the fate of each cell, frequently using toggle-like regulatory components. Synthetic biologists have long sought to recapitulate patterned differentiation with engineered cellular communities, and various methods for differentiating bacteria have been invented. Here, we couple a synthetic corepressive toggle switch with intercellular signaling pathways to create a "quorum-sensing toggle". We show that this circuit not only exhibits population-wide bistability in a well-mixed liquid environment but also generates patterns of differentiation in colonies grown on agar containing an externally supplied morphogen. If coupled to other metabolic processes, circuits such as the one described here would allow for the engineering of spatially patterned, differentiated bacteria for use in biomaterials and bioelectronics.
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Affiliation(s)
| | - Gaoyang Fan
- Department of Mathematics, University of Houston, Houston, Texas 77204, United States
| | - Eduardo Sontag
- Department of Bioengineering and Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, Texas 77204, United States
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
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2
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Fedorec AJH, Treloar NJ, Wen KY, Dekker L, Ong QH, Jurkeviciute G, Lyu E, Rutter JW, Zhang KJY, Rosa L, Zaikin A, Barnes CP. Emergent digital bio-computation through spatial diffusion and engineered bacteria. Nat Commun 2024; 15:4896. [PMID: 38851790 PMCID: PMC11162413 DOI: 10.1038/s41467-024-49264-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
Biological computing is a promising field with potential applications in biosafety, environmental monitoring, and personalized medicine. Here we present work on the design of bacterial computers using spatial patterning to process information in the form of diffusible morphogen-like signals. We demonstrate, mathematically and experimentally, that single, modular, colonies can perform simple digital logic, and that complex functions can be built by combining multiple colonies, removing the need for further genetic engineering. We extend our experimental system to incorporate sender colonies as morphogen sources, demonstrating how one might integrate different biochemical inputs. Our approach will open up ways to perform biological computation, with applications in bioengineering, biomaterials and biosensing. Ultimately, these computational bacterial communities will help us explore information processing in natural biological systems.
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Affiliation(s)
- Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
| | - Neythen J Treloar
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Ke Yan Wen
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Linda Dekker
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Qing Hsuan Ong
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Gabija Jurkeviciute
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Enbo Lyu
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Jack W Rutter
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Kathleen J Y Zhang
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Luca Rosa
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Alexey Zaikin
- Department of Mathematics, University College London, London, WC1E 6BT, UK
- Institute for Women's Health, University College London, London, WC1E 6BT, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
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3
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Kretschmer S, Perry N, Zhang Y, Kortemme T. Multi-input Drug-Controlled Switches of Mammalian Gene Expression Based on Engineered Nuclear Hormone Receptors. ACS Synth Biol 2023; 12:1924-1934. [PMID: 37315218 PMCID: PMC10367131 DOI: 10.1021/acssynbio.3c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Indexed: 06/16/2023]
Abstract
Protein-based switches that respond to different inputs to regulate cellular outputs, such as gene expression, are central to synthetic biology. For increased controllability, multi-input switches that integrate several cooperating and competing signals for the regulation of a shared output are of particular interest. The nuclear hormone receptor (NHR) superfamily offers promising starting points for engineering multi-input-controlled responses to clinically approved drugs. Starting from the VgEcR/RXR pair, we demonstrate that novel (multi)drug regulation can be achieved by exchange of the ecdysone receptor (EcR) ligand binding domain (LBD) for other human NHR-derived LBDs. For responses activated to saturation by an agonist for the first LBD, we show that outputs can be boosted by an agonist targeting the second LBD. In combination with an antagonist, output levels are tunable by up to three simultaneously present small-molecule drugs. Such high-level control validates NHRs as a versatile, engineerable platform for programming multidrug-controlled responses.
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Affiliation(s)
- Simon Kretschmer
- Department
of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- California
Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, California 94158, United States
| | - Nicholas Perry
- Department
of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- California
Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, California 94158, United States
- University
of California, Berkeley—University of California, San Francisco
Joint Graduate Program in Bioengineering, San Francisco, California 94158, United States
| | - Yang Zhang
- Department
of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- California
Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, California 94158, United States
| | - Tanja Kortemme
- Department
of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- California
Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, California 94158, United States
- University
of California, Berkeley—University of California, San Francisco
Joint Graduate Program in Bioengineering, San Francisco, California 94158, United States
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4
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Milner PT, Zhang Z, Herde ZD, Vedire NR, Zhang F, Realff MJ, Wilson CJ. Performance Prediction of Fundamental Transcriptional Programs. ACS Synth Biol 2023; 12:1094-1108. [PMID: 36935615 PMCID: PMC10127286 DOI: 10.1021/acssynbio.2c00593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Transcriptional programming leverages systems of engineered transcription factors to impart decision-making (e.g., Boolean logic) in chassis cells. The number of components used to construct said decision-making systems is rapidly increasing, making an exhaustive experimental evaluation of iterations of biological circuits impractical. Accordingly, we posited that a predictive tool is needed to guide and accelerate the design of transcriptional programs. The work described here involves the development and experimental characterization of a large collection of network-capable single-INPUT logical operations─i.e., engineered BUFFER (repressor) and engineered NOT (antirepressor) logical operations. Using this single-INPUT data and developed metrology, we were able to model and predict the performances of all fundamental two-INPUT compressed logical operations (i.e., compressed AND gates and compressed NOR gates). In addition, we were able to model and predict the performance of compressed mixed phenotype logical operations (A NIMPLY B gates and complementary B NIMPLY A gates). These results demonstrate that single-INPUT data is sufficient to accurately predict both the qualitative and quantitative performance of a complex circuit. Accordingly, this work has set the stage for the predictive design of transcriptional programs of greater complexity.
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Affiliation(s)
- Prasaad T Milner
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Ziqiao Zhang
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Zachary D Herde
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Namratha R Vedire
- School of Computer Science, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Fumin Zhang
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Matthew J Realff
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
| | - Corey J Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-2000, United States
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5
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Kretschmer S, Perry N, Zhang Y, Kortemme T. Multi-input drug-controlled switches of mammalian gene expression based on engineered nuclear hormone receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526549. [PMID: 36778233 PMCID: PMC9915577 DOI: 10.1101/2023.02.01.526549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Protein-based switches that respond to different inputs to regulate cellular outputs, such as gene expression, are central to synthetic biology. For increased controllability, multi-input switches that integrate several cooperating and competing signals for the regulation of a shared output are of particular interest. The nuclear hormone receptor (NHR) superfamily offers promising starting points for engineering multi-input-controlled responses to clinically approved drugs. Starting from the VgEcR/RXR pair, we demonstrate that novel (multi-)drug regulation can be achieved by exchange of the ecdysone receptor (EcR) ligand binding domain (LBD) for other human NHR-derived LBDs. For responses activated to saturation by an agonist for the first LBD, we show that outputs can be boosted by an agonist targeting the second LBD. In combination with an antagonist, output levels are tunable by up to three simultaneously present small-molecule drugs. Such high-level control validates NHRs as a versatile, engineerable platform for programming multi-drug-controlled responses.
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Affiliation(s)
- Simon Kretschmer
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- California Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, CA 94158, USA
| | - Nicholas Perry
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- California Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, CA 94158, USA
- University of California, Berkeley—University of California, San Francisco Joint Graduate Program in Bioengineering, San Francisco, CA, USA
| | - Yang Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- California Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, CA 94158, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- California Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, CA 94158, USA
- University of California, Berkeley—University of California, San Francisco Joint Graduate Program in Bioengineering, San Francisco, CA, USA
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Anderson DA, Voigt CA. Competitive dCas9 binding as a mechanism for transcriptional control. Mol Syst Biol 2021; 17:e10512. [PMID: 34747560 PMCID: PMC8574044 DOI: 10.15252/msb.202110512] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
Catalytically dead Cas9 (dCas9) is a programmable transcription factor that can be targeted to promoters through the design of small guide RNAs (sgRNAs), where it can function as an activator or repressor. Natural promoters use overlapping binding sites as a mechanism for signal integration, where the binding of one can block, displace, or augment the activity of the other. Here, we implemented this strategy in Escherichia coli using pairs of sgRNAs designed to repress and then derepress transcription through competitive binding. When designed to target a promoter, this led to 27-fold repression and complete derepression. This system was also capable of ratiometric input comparison over two orders of magnitude. Additionally, we used this mechanism for promoter sequence-independent control by adopting it for elongation control, achieving 8-fold repression and 4-fold derepression. This work demonstrates a new genetic control mechanism that could be used to build analog circuit or implement cis-regulatory logic on CRISPRi-targeted native genes.
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Affiliation(s)
- Daniel A Anderson
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Christopher A Voigt
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
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7
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Tietze L, Lale R. Importance of the 5' regulatory region to bacterial synthetic biology applications. Microb Biotechnol 2021; 14:2291-2315. [PMID: 34171170 PMCID: PMC8601185 DOI: 10.1111/1751-7915.13868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/02/2023] Open
Abstract
The field of synthetic biology is evolving at a fast pace. It is advancing beyond single-gene alterations in single hosts to the logical design of complex circuits and the development of integrated synthetic genomes. Recent breakthroughs in deep learning, which is increasingly used in de novo assembly of DNA components with predictable effects, are also aiding the discipline. Despite advances in computing, the field is still reliant on the availability of pre-characterized DNA parts, whether natural or synthetic, to regulate gene expression in bacteria and make valuable compounds. In this review, we discuss the different bacterial synthetic biology methodologies employed in the creation of 5' regulatory regions - promoters, untranslated regions and 5'-end of coding sequences. We summarize methodologies and discuss their significance for each of the functional DNA components, and highlight the key advances made in bacterial engineering by concentrating on their flaws and strengths. We end the review by outlining the issues that the discipline may face in the near future.
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Affiliation(s)
- Lisa Tietze
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| | - Rahmi Lale
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
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8
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Design and Evaluation of Synthetic RNA-Based Incoherent Feed-Forward Loop Circuits. Biomolecules 2021; 11:biom11081182. [PMID: 34439849 PMCID: PMC8391864 DOI: 10.3390/biom11081182] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/31/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022] Open
Abstract
RNA-based regulators are promising tools for building synthetic biological systems that provide a powerful platform for achieving a complex regulation of transcription and translation. Recently, de novo-designed synthetic RNA regulators, such as the small transcriptional activating RNA (STAR), toehold switch (THS), and three-way junction (3WJ) repressor, have been utilized to construct RNA-based synthetic gene circuits in living cells. In this work, we utilized these regulators to construct type 1 incoherent feed-forward loop (IFFL) circuits in vivo and explored their dynamic behaviors. A combination of a STAR and 3WJ repressor was used to construct an RNA-only IFFL circuit. However, due to the fast kinetics of RNA–RNA interactions, there was no significant timescale difference between the direct activation and the indirect inhibition, that no pulse was observed in the experiments. These findings were confirmed with mechanistic modeling and simulation results for a wider range of conditions. To increase delay in the inhibition pathway, we introduced a protein synthesis process to the circuit and designed an RNA–protein hybrid IFFL circuit using THS and TetR protein. Simulation results indicated that pulse generation could be achieved with this RNA–protein hybrid model, and this was further verified with experimental realization in E. coli. Our findings demonstrate that while RNA-based regulators excel in speed as compared to protein-based regulators, the fast reaction kinetics of RNA-based regulators could also undermine the functionality of a circuit (e.g., lack of significant timescale difference). The agreement between experiments and simulations suggests that the mechanistic modeling can help debug issues and validate the hypothesis in designing a new circuit. Moreover, the applicability of the kinetic parameters extracted from the RNA-only circuit to the RNA–protein hybrid circuit also indicates the modularity of RNA-based regulators when used in a different context. We anticipate the findings of this work to guide the future design of gene circuits that rely heavily on the dynamics of RNA-based regulators, in terms of both modeling and experimental realization.
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9
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Monteiro LMO, Sanches-Medeiros A, Westmann CA, Silva-Rocha R. Unraveling the Complex Interplay of Fis and IHF Through Synthetic Promoter Engineering. Front Bioeng Biotechnol 2020; 8:510. [PMID: 32626694 PMCID: PMC7314903 DOI: 10.3389/fbioe.2020.00510] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/30/2020] [Indexed: 02/03/2023] Open
Abstract
Bacterial promoters are usually formed by multiple cis-regulatory elements recognized by a plethora of transcriptional factors (TFs). From those, global regulators are key elements since these TFs are responsible for the regulation of hundreds of genes in the bacterial genome. For instance, Fis and IHF are global regulators that play a major role in gene expression control in Escherichia coli, and usually, multiple cis-regulatory elements for these proteins are present at target promoters. Here, we investigated the relationship between the architecture of the cis-regulatory elements for Fis and IHF in E. coli. For this, we analyze 42 synthetic promoter variants harboring consensus cis-elements for Fis and IHF at different distances from the core -35/-10 region and in various numbers and combinations. We first demonstrated that although Fis preferentially recognizes its consensus cis-element, it can also recognize, to some extent, the consensus-binding site for IHF, and the same was true for IHF, which was also able to recognize Fis binding sites. However, changing the arrangement of the cis-elements (i.e., the position or number of sites) can completely abolish the non-specific binding of both TFs. More remarkably, we demonstrated that combining cis-elements for both TFs could result in Fis and IHF repressed or activated promoters depending on the final architecture of the promoters in an unpredictable way. Taken together, the data presented here demonstrate how small changes in the architecture of bacterial promoters could result in drastic changes in the final regulatory logic of the system, with important implications for the understanding of natural complex promoters in bacteria and their engineering for novel applications.
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Affiliation(s)
| | | | - Cauã Antunes Westmann
- Ribeirão Preto Medical School (FMRP), University of São Paulo, Ribeirão Preto, Brazil
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School (FMRP), University of São Paulo, Ribeirão Preto, Brazil
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10
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Li N, Zeng W, Xu S, Zhou J. Obtaining a series of native gradient promoter-5'-UTR sequences in Corynebacterium glutamicum ATCC 13032. Microb Cell Fact 2020; 19:120. [PMID: 32493332 PMCID: PMC7268698 DOI: 10.1186/s12934-020-01376-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/25/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Corynebacterium glutamicum is an important industrial microorganism used for the production of many valuable compounds, especially amino acids and their derivatives. For fine-tuning of metabolic pathways, synthetic biological tools are largely based on the rational application of promoters. However, the limited number of promoters make it difficult. RESULTS In this study, according to the analysis of RNA-Seq data, 90 DNA fragments with lengths of 200-500 bp that may contain promoter-5'-UTR (PUTR) sequences were amplified and linked to a fluorescent protein gene. When compared with the common strong PUTR PsodUTR, 17 strong PUTRs were obtained, which maintained stable expression strengths from the early to post stationary phase. Among them, PNCgl1676UTR was the strongest and its fluorescent protein expression level was more than five times higher than that of PsodUTR. Furthermore, nine typical chemicals related to the biosynthesis of sulfur-containing amino acids (such as L-methionine, L-cysteine) were selected as stress substances to preliminarily explore the stress on these PUTRs. The results showed that the expression of PbrnFUTR was activated by L-methionine, while that of PNCgl1202UTR was severely inhibited by L-lysine. CONCLUSIONS These findings demonstrated that the selected PUTRs can stably express different genes, such as the red fluorescence protein gene, and can be useful for fine-tuning regulation of metabolic networks in C. glutamicum or for establishing high-throughput screening strategies through biosensor for the production of useful compounds.
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Affiliation(s)
- Ning Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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11
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Shin J, Zhang S, Der BS, Nielsen AAK, Voigt CA. Programming Escherichia coli to function as a digital display. Mol Syst Biol 2020; 16:e9401. [PMID: 32141239 PMCID: PMC7058928 DOI: 10.15252/msb.20199401] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 01/18/2023] Open
Abstract
Synthetic genetic circuits offer the potential to wield computational control over biology, but their complexity is limited by the accuracy of mathematical models. Here, we present advances that enable the complete encoding of an electronic chip in the DNA carried by Escherichia coli (E. coli). The chip is a binary-coded digit (BCD) to 7-segment decoder, associated with clocks and calculators, to turn on segments to visualize 0-9. Design automation is used to build seven strains, each of which contains a circuit with up to 12 repressors and two activators (totaling 63 regulators and 76,000 bp DNA). The inputs to each circuit represent the digit to be displayed (encoded in binary by four molecules), and output is the segment state, reported as fluorescence. Implementation requires an advanced gate model that captures dynamics, promoter interference, and a measure of total power usage (RNAP flux). This project is an exemplar of design automation pushing engineering beyond that achievable "by hand", essential for realizing the potential of biology.
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Affiliation(s)
- Jonghyeon Shin
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Shuyi Zhang
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Bryan S Der
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Alec AK Nielsen
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Christopher A Voigt
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
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12
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Wang J, Deng K, Zhou C, Fang Z, Meyer C, Deshpande KUA, Li Z, Mi X, Luo Q, Hammock BD, Tan C, Chen Y, Pan T. Microfluidic cap-to-dispense (μCD): a universal microfluidic-robotic interface for automated pipette-free high-precision liquid handling. LAB ON A CHIP 2019; 19:3405-3415. [PMID: 31501848 PMCID: PMC6785371 DOI: 10.1039/c9lc00622b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Microfluidic devices have been increasingly used for low-volume liquid handling operations. However, laboratory automation of such delicate devices has lagged behind due to the lack of world-to-chip (macro-to-micro) interfaces. In this paper, we have presented the first pipette-free robotic-microfluidic interface using a microfluidic-embedded container cap, referred to as a microfluidic cap-to-dispense (μCD), to achieve a seamless integration of liquid handling and robotic automation without any traditional pipetting steps. The μCD liquid handling platform offers a generic and modular way to connect the robotic device to standard liquid containers. It utilizes the high accuracy and high flexibility of the robotic system to recognize, capture and position; and then using microfluidic adaptive printing it can achieve high-precision on-demand volume distribution. With its modular connectivity, nanoliter processability, high adaptability, and multitask capacity, μCD shows great potential as a generic robotic-microfluidic interface for complete pipette-free liquid handling automation.
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Affiliation(s)
- Jingjing Wang
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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13
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Yim SS, Johns NI, Park J, Gomes ALC, McBee RM, Richardson M, Ronda C, Chen SP, Garenne D, Noireaux V, Wang HH. Multiplex transcriptional characterizations across diverse bacterial species using cell-free systems. Mol Syst Biol 2019; 15:e8875. [PMID: 31464371 PMCID: PMC6692573 DOI: 10.15252/msb.20198875] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/01/2019] [Accepted: 07/03/2019] [Indexed: 12/14/2022] Open
Abstract
Cell-free expression systems enable rapid prototyping of genetic programs in vitro. However, current throughput of cell-free measurements is limited by the use of channel-limited fluorescent readouts. Here, we describe DNA Regulatory element Analysis by cell-Free Transcription and Sequencing (DRAFTS), a rapid and robust in vitro approach for multiplexed measurement of transcriptional activities from thousands of regulatory sequences in a single reaction. We employ this method in active cell lysates developed from ten diverse bacterial species. Interspecies analysis of transcriptional profiles from > 1,000 diverse regulatory sequences reveals functional differences in promoter activity that can be quantitatively modeled, providing a rich resource for tuning gene expression in diverse bacterial species. Finally, we examine the transcriptional capacities of dual-species hybrid lysates that can simultaneously harness gene expression properties of multiple organisms. We expect that this cell-free multiplex transcriptional measurement approach will improve genetic part prototyping in new bacterial chassis for synthetic biology.
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Affiliation(s)
- Sung Sun Yim
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Nathan I Johns
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
- Present address:
Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Jimin Park
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
| | - Antonio LC Gomes
- Department of ImmunologyMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Ross M McBee
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Department of Biological SciencesColumbia UniversityNew YorkNYUSA
| | - Miles Richardson
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
| | - Carlotta Ronda
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Sway P Chen
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
| | - David Garenne
- School of Physics and AstronomyUniversity of MinnesotaMinneapolisMNUSA
| | - Vincent Noireaux
- School of Physics and AstronomyUniversity of MinnesotaMinneapolisMNUSA
| | - Harris H Wang
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNYUSA
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